Process raw biomass data from one harvest

This function processes the raw biomass data stored in a harvest_point object to convert it into more meaningful values.

Usage

process(x, ...)

  # S3 method for class 'harvest_point'
process(x, leaf_name = 'leaf', ...)

Arguments

x: A harvest_point object.
leaf_name: A string specifying the name of the leaf tissue to use when calculating the leaf area index. Typically, the leaf mass is called 'leaf', but it may sometimes have a similar name such as 'main_leaf'.
...: Additional arguments (currently unused).

Details

The process function attempts to make a variety of calculations using the information stored in x. If some of the possible elements of x are set to NA, the relevant calculations that would require those pieces of information will simply be skipped, and their outputs will be set to NA. The results of the calculations will be stored as new elements in the harvest_point object.

The detailed calculations are as follows:

time: In BioCro, the time is specified as a fractional day of the year calculated by time = doy + hour / 24.0.
measured_population: The number of plants per unit ground area (in plants / acre can be estimated from the row spacing and the number of plants harvested for above-ground biomass using measured_population = agb_nplants / (agb_row_length * row_spacing) * 4047. Here, the factor 4047 converts the area basis from m^2 to acre using 1 acre = 4047 m^2.
agb_per_area: The amount of above-ground biomass per unit ground area (in Mg / ha) in the plot can be estimated from the row spacing and the dry mass of the plants harvested for above-ground biomass using agb_per_area = agb_weight / (agb_row_length * row_spacing) * 1e-2. Here, the factor 1e-2 converts from g / m^2 to Mg / ha using 1 g / m^2 = 0.01 Mg / ha.
agb_per_plant_row: The amount of above-ground biomass per plant (in g / plant) can be estimated from the row section harvested for above-ground biomass using agb_per_plant_row = agb_weight / agb_nplants. This value can be compared against agb_per_plant_partitioning to get an idea of the variability in plant size throughout the plot.
partitioning_agb_weight: The above-ground biomass (in g) of the plants selected for partitioning can be obtained by adding the partitioning component weights for the components that are designated as being part of the above-ground biomass. For example, if partitioning_component_weights = list(leaf = 1, stem = 2, root = 0.5) and agb_components = c('leaf', 'stem'), then the above-ground biomass from the partitioned plants would be 1 + 2 = 3. In other words, the root mass would not be included.
agb_per_plant_partitioning: The amount of above-ground biomass per plant (in g / plant) can be estimated from the partitioned plants using agb_per_plant_partitioning = partitioning_agb_weight / agb_nplants. This value can be compared against agb_per_plant_row to get an idea of the variability in plant size throughout the plot.
relative_components: The relative mass (dimensionless from g / g; normalized to the above-ground biomass) for each partitioned component can be obtained by dividing each component's dry mass by partitioning_agb_weight. For example, if partitioning_component_weights = list(leaf = 1, stem = 2, root = 0.5) and agb_components = c('leaf', 'stem'), then partitioning_agb_weight = 3 and relative_components = list(leaf = 1 / 3, stem = 2 / 3, root = 0.5 / 3).
components_biocro: The biomass per unit ground area (in Mg / ha, the units used in BioCro) can be obtained by multiplying each element of relative_components by agb_per_area.
LMA: The leaf mass per unit leaf area (LMA; in units of g / m^2) can be calculated from the mass and area of the partitioned leaves using LMA = partitioning_component_weights$leaf / partitioning_leaf_area * 1e4. Here, the factor 1e-4 converts from g / cm^2 to g / m^2 using 1 g / cm^2 = 1e-4 g / m^2.
LAI_from_LMA: The leaf area per unit ground area, which is referred to as the leaf area index (LAI; dimensionless from m^2 / m^2), can be calculated from the leaf mass per unit area and the LMA using LAI = components_biocro$leaf / LMA * 1e2. Here, the factor 1e2 converts the leaf mass per unit area from Mg / ha to g / m^2 using 1 Mg / ha = 100 g / m^2. This estimate of LAI can be compared to the estimates based on planting density or measured population, which are stored as LAI_from_planting_density and LAI_from_measured_population, respectively.
leaf_area_per_plant: The leaf area per plant in cm^2 / plant can be calculated from the partitioning leaf area and the number of plants that were partitioned.
LAI_from_planting_density: The LAI can be estimated from the planting density and the leaf area per plant using LAI = planting_density * leaf_area_per_plant * 1e-4 / 4047. Here, the factor 1e-4 converts leaf area from cm^2 to m^2 and the factor 1 / 4047 converts population from plants / acre to plants / m^2. This estimate of LAI can be compared to the estimates based on LMA or measured population, which are stored as LAI_from_LMA and LAI_from_measured_population, respectively.
LAI_from_measured_population: The LAI can be estimated from the measured population and the leaf area per plant using LAI = measured_population * leaf_area_per_plant * 1e-4. Here, the factor 1e-4 converts leaf area from cm^2 to m^2. This estimate of LAI can be compared to the estimates based on LMA or planting density, which are stored as LAI_from_LMA and LAI_from_planting_density, respectively.
SLA: The leaf mass per unit leaf area, which is referred to as the specific leaf area (SLA; in units of ha / Mg), can be calculated from LMA using SLA = 1 / LMA * 1e2 where the factor 1e2 converts the units from m^2 / g to ha / Mg.
trap_components_biocro: The biomass per unit ground area for the tissue types collected in the litter trap (in units of Mg / ha) can be calculated by dividing the dry mass of each component by the litter trap area and multiplying by 1e-2 to convert from g / m^2 to Mg / ha.
all_components_biocro: The biomass per unit ground area (in Mg / ha) for all plant tissue types included in components_biocro and trap_components_biocro is stored in all_components_biocro. If a component is present in both lists, the separate values will be added together. For example, components_biocro may include a leaf_litter component that represents the biomass of senesced leaves that are still attached to the plants, while trap_components_biocro may contain a leaf_litter component representing the biomass of senesced leaves that have fallen off the plant; in this case, the value of leaf_litter in all_components_biocro will be the sum of the two separate leaf litter biomass values.

A note about LAI estimates: LAI estimated using LMA is the most accurate of the three methods, and is commonly used when estimating LAI from destructive leaf area measurements (Bréda 2003). When mass values are unavailable, it may not be possible to use this method; in that case, the estimates based on population can be used instead. When enough information is available to make all three estimates, they can be compared to each other as a consistency check or to estimate upper and lower bounds on the LAI.

References:

Bréda, N. J. J. "Ground-based measurements of leaf area index: a review of methods, instruments and current controversies." Journal of Experimental Botany 54, 2403–2417 (2003) [doi:10.1093/jxb/erg263 ].

Value

A harvest_point object with new elements as described above.

Examples